Virome identification in wheat in the Czech Republic using small RNA deep sequencing
High-throughput deep-sequencing technology and bioinformatics analysis of the small RNA (sRNA) population isolated from plants allows universal virus detection and complete virome reconstruction for a given sample. In the present sRNA deep-sequencing analysis of virus-infected wheat samples in the C...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Elsevier
2020-07-01
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| Series: | Journal of Integrative Agriculture |
| Subjects: | |
| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311919628054 |
| _version_ | 1818573730965618688 |
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| author | Khushwant SINGH Jana JAROŠOVÁ Jan FOUSEK Huan CHEN Jiban Kumar KUNDU |
| author_facet | Khushwant SINGH Jana JAROŠOVÁ Jan FOUSEK Huan CHEN Jiban Kumar KUNDU |
| author_sort | Khushwant SINGH |
| collection | DOAJ |
| description | High-throughput deep-sequencing technology and bioinformatics analysis of the small RNA (sRNA) population isolated from plants allows universal virus detection and complete virome reconstruction for a given sample. In the present sRNA deep-sequencing analysis of virus-infected wheat samples in the Czech Republic, samples were firstly tested for barley yellow dwarf viruses (BYDVs), wheat streak mosaic virus (WSMV) and wheat dwarf virus (WDV) using ELISA, RT-PCR and PCR. Subsequent sRNA sequencing of these samples yielded more than ~60 million single-end 50-bp reads with high confidence for nine field samples of wheat. Overall, 16.5% of reads were virus-specific and 83.5% were mapped to the host. More 21-nt reads (~7.7E+06 reads) were found than 24-nt (~6.20E+06 reads) or 22-nt (~4.30E+06 reads) reads. De novo assembly of the high-quality contigs revealed the presence of three earlier reported viruses in the Czech Republic: BYDVs (31.48%), WSMV (24.23%) and WDV (26.66%). We also showed the presence of cereal yellow dwarf virus (14.33%; two species CYDV-RPS and CYDV-RPV (family Luteoviridae/Polerovirus) and wheat yellow dwarf virus (WYDV, 3.30%; Luteoviridae). Phylogenetic analysis showed CYDV and WYDV grouped separately from BYDVs. Furthermore, several recombination breakpoints were found among the groups of yellow dwarf viruses (BYDVs, CYDV, and WYDV). Using RNA deep sequencing, we confirmed the presence of the three known viruses (BYDVs, WSMV, and WDV) and the first record of two species of CYDV and WYDV in wheat in the Czech Republic. |
| first_indexed | 2024-12-15T00:16:48Z |
| format | Article |
| id | doaj.art-87de7d49da6c4c74a202755822098d22 |
| institution | Directory Open Access Journal |
| issn | 2095-3119 |
| language | English |
| last_indexed | 2024-12-15T00:16:48Z |
| publishDate | 2020-07-01 |
| publisher | Elsevier |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj.art-87de7d49da6c4c74a202755822098d222022-12-21T22:42:26ZengElsevierJournal of Integrative Agriculture2095-31192020-07-0119718251833Virome identification in wheat in the Czech Republic using small RNA deep sequencingKhushwant SINGH0Jana JAROŠOVÁ1Jan FOUSEK2Huan CHEN3Jiban Kumar KUNDU4Plant Virus and Vector Interactions Group, Division of Crop Protection and Plant Health, Crop Research Institute, Prague 16106, Czech RepublicPlant Virus and Vector Interactions Group, Division of Crop Protection and Plant Health, Crop Research Institute, Prague 16106, Czech RepublicPlant Virus and Vector Interactions Group, Division of Crop Protection and Plant Health, Crop Research Institute, Prague 16106, Czech RepublicZhejiang Tianke High-Technology Development Co., Ltd., Hangzhou 310012, P.R. ChinaPlant Virus and Vector Interactions Group, Division of Crop Protection and Plant Health, Crop Research Institute, Prague 16106, Czech Republic; Correspondence Jiban Kumar KUNDUHigh-throughput deep-sequencing technology and bioinformatics analysis of the small RNA (sRNA) population isolated from plants allows universal virus detection and complete virome reconstruction for a given sample. In the present sRNA deep-sequencing analysis of virus-infected wheat samples in the Czech Republic, samples were firstly tested for barley yellow dwarf viruses (BYDVs), wheat streak mosaic virus (WSMV) and wheat dwarf virus (WDV) using ELISA, RT-PCR and PCR. Subsequent sRNA sequencing of these samples yielded more than ~60 million single-end 50-bp reads with high confidence for nine field samples of wheat. Overall, 16.5% of reads were virus-specific and 83.5% were mapped to the host. More 21-nt reads (~7.7E+06 reads) were found than 24-nt (~6.20E+06 reads) or 22-nt (~4.30E+06 reads) reads. De novo assembly of the high-quality contigs revealed the presence of three earlier reported viruses in the Czech Republic: BYDVs (31.48%), WSMV (24.23%) and WDV (26.66%). We also showed the presence of cereal yellow dwarf virus (14.33%; two species CYDV-RPS and CYDV-RPV (family Luteoviridae/Polerovirus) and wheat yellow dwarf virus (WYDV, 3.30%; Luteoviridae). Phylogenetic analysis showed CYDV and WYDV grouped separately from BYDVs. Furthermore, several recombination breakpoints were found among the groups of yellow dwarf viruses (BYDVs, CYDV, and WYDV). Using RNA deep sequencing, we confirmed the presence of the three known viruses (BYDVs, WSMV, and WDV) and the first record of two species of CYDV and WYDV in wheat in the Czech Republic.http://www.sciencedirect.com/science/article/pii/S2095311919628054NGSsRNABYDVsCYDVWSMVWYDV |
| spellingShingle | Khushwant SINGH Jana JAROŠOVÁ Jan FOUSEK Huan CHEN Jiban Kumar KUNDU Virome identification in wheat in the Czech Republic using small RNA deep sequencing Journal of Integrative Agriculture NGS sRNA BYDVs CYDV WSMV WYDV |
| title | Virome identification in wheat in the Czech Republic using small RNA deep sequencing |
| title_full | Virome identification in wheat in the Czech Republic using small RNA deep sequencing |
| title_fullStr | Virome identification in wheat in the Czech Republic using small RNA deep sequencing |
| title_full_unstemmed | Virome identification in wheat in the Czech Republic using small RNA deep sequencing |
| title_short | Virome identification in wheat in the Czech Republic using small RNA deep sequencing |
| title_sort | virome identification in wheat in the czech republic using small rna deep sequencing |
| topic | NGS sRNA BYDVs CYDV WSMV WYDV |
| url | http://www.sciencedirect.com/science/article/pii/S2095311919628054 |
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